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If I recall correctly, the clonetroopers on Mustafar in the Ep3 game's alternate ending seemed to accept Vader's claim of lordship over the Emperor. Theoretically, it's likely that they were conditioned to accept the Sith way of Apprentice overcoming the Master, and then rather than kill the "traitor", follow him instead. They followed a Sith Lord like Palpy without question, after all.
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